The Mystery of the Borealis
by JbearInChief
Summary: Jenna Brandenburgh has a flashback that reveals the mystery behind Aperture Sciences' Borealis. Why it's important to not only the resistance, but to the combine. And if Gordon and Alyx don't get to it first, we may not stand a chance. T For language


**Hello everyone! JBearinChief here. I know it's been forever since I've uploaded anything, but college is a pain in the ass. I had to write a 20-page paper on **_**The Daily Show **_**so that took up most of the time from May until now. **

**BUT with the semester out of the way, I got to writing more half-life fanfics again! here is another part of the post-resonance cascade (aka Half-life 2 timeline) part of "Barney, the HECU, and the Black Mesa Incident." Unfortunately, it's not a whole lot of Barney, but more a flashback from one of Jenna Brandenburgh's missions as a marine. It explains what I personally think is going on with the Borealis and why it's so important to both the Combine and the Resistance. We will see (hopefully soon) if episode 3 proves my theory correct. Hope you all enjoy and reviews are warmly welcomed! *fuzzy feelings!* **

Jenna went back to her room. Kleiner seemed excited about seeing what's on the Borealis, but Jenna had a very dark feeling in her stomach. She knew there had to be a reason the combine were pursuing the Borealis as well, but she couldn't figure out what. Even Mossman couldn't understand what the Borealis contained. Unfortunately, that made it even worse. The Borealis contained science that even Judith Mossman, a PhD in physics, couldn't comprehend. Jenna feared that it was something very dangerous and very powerful. She slumped into her bed and slowly drifted asleep.

But her dream put her into a flashback from her life as a marine…….

Jenna and Adrian sat in the briefing room. Jackson and Tower were bickering behind them, as they usually did.

"Listen up," Captain Miller said, "We have a mission out in Utah. This is not a drill. We've received a distress call from a place called Aperture Science Laboratories. The scientists and employees are being killed. All police and army personnel cannot secure the building because there is reason to believe a biological toxin has been released into the air."

"Great, we're baby-sitting some dumbass scientists who can't do their jobs right?" Jackson mumbled behind them.

"Ya," Tower agreed, "They spilled some drain cleaner in the building and send out an S.O.S. What a bunch of crap."

"Is there something you would like to share with the rest of us, Tower?"

"No, sir." Tower replied in military form.

"Maybe it is your mother sending out an S.O.S. because her son is such a worthless pile of crap!" Captain Miller said.

Jackson snorted with laughter.

"And YOU, Jackson," Miller snapped, "Maybe you and your girlfriend Tower should stay behind and scrub the floor like women, would you like that?"

"No, SIR," Jackson said.

"Then you and Tower need to SHUT UP!"

Adrian smirked next to Jenna, but was careful not to make a sound.

"We will leave in exactly 1 hour. Full gear, no exceptions. Anyone late will be left behind. Am I clear?"

"Yes SIR!" The squad said.

"Dismissed!" Captain Miller said.

After a long helicopter ride, the squads landed at Aperture Science on the rooftop helipads. The squads got out and made their way down the exterior ladders to the front of the building. All units met up and waited until Captain Miller finally spoke.

"Alright, ladies," He said, "We got a distress signal from the scientists in here. Team Omega is currently obtaining members of the science team from a nearby hospital and will rendezvous here with the scientist in approximately 20 minutes. In the meantime you all are to go in there and find any distressed scientists and extract them ASAP."

"GOD! A search and rescue mission!" Tower grumbled. Jenna couldn't help but agree.

"Not listen up," Miller barked, "We have absolutely no idea what has caused this situation. We believe it to be a chemical spill, so make sure ALL equipment is installed properly, fully powered, and secured to your body. I will NOT be dragging you sorry asses out of there because you are too incompetent to put on your own mask! Am I clear?"

"Yes sir," the squads all cadenced.

"Epsilon team will be command. You will be out here directing radios and waiting for omega team to bring us the scientists. Now everyone follow me."

The squads all double checked their gear and followed the captain. Miller went to the biggest door on the building. He scanned his military ID card and the door obediently opened for him. It was an airlock. Alpha team, bravo team, and delta team all crammed into the airlock. The door shut behind them and the door in front of them opened.

There wasn't any obvious signs of toxins. The air was clear. However, strewn right in front of the airlock door was dozens of dead scientists.

"Alpha, you take left wings, I will lead delta on the right. Bravo. You all check the bodies for any survivors. All survivors must be immediately taken outside."

"There's not gonna BE any survivors. A bravo team mumbled."

While the Bravo team checked all the bodies for any survivors, Jenna, Adrian, Tower, Jackson, and Sergeant Knight made their way left through a large test chamber. They were going to exit the chamber when suddenly something lunged around the corner and pushed Jackson to the ground.

It was a scientist, covered in blood on his chest. His eyes were wild and bloodshot, with small, contracted pupils. He was also screaming in an ear piercing cry of pain.

"JESUS! GET IT OFF ME!" Jackson screamed.

"We have hostiles," Sergeant Knight yelled into the radio, "Requesting permission to engage."

"Negative unless armed," the commander said. "You must subdue them. They are unarmed scientists in there."

Jenna, Adrian and Tower grabbed the scientist and threw him to the ground. It got back up and charged Tower. Tower ran backwards until Tower tackled the scientist to the ground.

Tower wrestled around with the scientist, who flared his limbs wildly about.

"Command this is Alpha unit, we cannot subdue these hostiles. Requesting permission to engage…."

He suddenly stopped talking when he saw the scientist convulse on the floor. Tower sprang up and backed away cautiously. The scientist suddenly stopped breathing and went limp.

"What the hell…." Adrian said, looking at the now dead scientist.

Suddenly two scientists ran into the room after them. Both were foaming from the mouth and screaming violently. They ran towards them but ran over the dead scientist on the floor and tripped, sending both plummeting to the floor.

One of the scientists cracked his head and died instantly. The other convulsed for a moment and died like the first scientist.

"JESUS!" Jackson said.

Knight called through his radio to the command center outside.

"Does anyone have any idea what the hell is going on around here?"

"Negative," the radio controller said, "All units be advised to NOT engage scientists. Please subdue any personnel until further instructions."

"They're all dropping dead right in front of us!" The leader from Delta team yelled over the radio.

"They must be under something," Jenna chimed in over the radio, "The neurotoxin must be inhibiting their judgement."

"Any idea what it could be?"

"Radio command, this is lutennant Mitchell. I don't know what the hell is going on, but we have hostiles down here. They look like….zombies or something. They have strange eyes, foaming from the mouth. We have locked them in the labs while awaiting orders, over."

"10-4, Mitchell. We are trying to figure out the source of the poisoning now," the radio controller said, "Could it be cyanide poisoning?"

"Negative, radio command," Jenna said, "They would be lethargic and weak. These hostiles are violent and frantic."

Suddenly, Jenna had a flash from an advanced biology course she took not too long ago for her degree.

"Radio command, can someone test the air for Sarin levels?"

"10-4, Corporal Brandenburgh. Orders to shoot any hostiles until further information is received." The command said.

"Well Congratulations, Corporal Brandenburgh," came a robotic voice, "You have solved the mystery. It is a sarin derivative used to advance the Aperture Science Heimlich counter-maneuver project."

The squad looked around, guns at the ready.

It was a P.A. system, with a very robotic, yet intimidating woman's voice.

"Radio command," Knight said, "We have interaction with some sort of automated message system. Can you confirm?"

"Negative," radio command said, "We have the science team here now. They confirm that the toxin is sarin, and have informed us that the voice it is their disc operating system. It is not automated, but actually interactive. Her name is Gladys."

"I am the Genetic Lifeform and Disk Operating System, GlaDos. I oversee all aperture science enrichment center activities and provide cake and grief counseling after all enrichment center tests."

Jenna looked at her Adrian. Through his mask, Jenna could see his brow furrow with confusion. He looked back at Jenna, who shrugged, being equally confused.

"Command to unit 12," the commander said, addressing Jenna's unit, "We are bringing in the science team. They say they can get the machine to stop flooding the labs with the toxin. Unit alpha, be ready to intercept the team on the east main entrance."

"10-4 command," Knight said, "en route now."

They went back to the main entrance and waited. A team of four scientists, glad in full haz-mat suits came through a side door with two HECU marines.

"Need backup?" one of the two escorts asked.

"Negative," Knight said, "It seems like everyone in here is dead now."

"10-4" the escort said, "We'll be waiting for you on the other side."

Knight looked at the four scientists.

"Alright, boys," Knight said, "How are we going to fix this?"

"A…a morality core, sir," one of them mumbled.

"Come again?"

"A morality core. We've been working on it for a few months. We were going to install it tomorrow, but she obviously flooded the labs with Chemical-Y.

"You mean the sarin?" Jenna asked, very angry.

"It's derived from Sarin, but it's been modified. It's part of the Heimlich counter-maneuver project. It was meant to simulate choking but there are other side effects. It's still in development."

"Welcome, Doctors," Came GlaDos' robotic voice, "I've noted Chemical-Y as a failure. I have made changes to the compound structures to better ensure success in future tests. For celebration of the breakthrough, please direct yourselves to the kitchens for delicious cake."

"Can we get a move on? This thing is creeping me out," Knight said.

The scientists led the team into a storage area filled with what looked like hundreds of round white spheres. There was one in the middle, which was glowing purple in the center of the sphere.

The four scientists picked it up and led them through the storage room, through a door into an extremely large open room.

The scientists walked to the base of the machine to a small computer. One of them typed in a code that made the huge machine lower, almost to the ground.

"Please note that the installation of any hardware components will require me to re-boot, and will, therefore, run the risk of the cake becoming over baked."

"What's with this cake crap?" Adrian mumbled to Jenna.

"I dunno," she replied, "Must be some glitch, or inside joke or something."

The scientists were working on installing the sphere when suddenly, GlaDos, in an especially creepy, hostile voiced chimed with, "You're not even doing that correctly. Are you real doctors?"

The machine suddenly lurched upwards, causing the purple sphere to fall out.

A scientist whirled around to the computer and typed in some more information, and GlaDos came down again.

"Ha-ha-ha," It laughed in a strangely sinister way, "Just kidding. Be advised that all aperture science personnel are highly qualified in their field of expertise. Unfortunately, most of the personnel are dead."

Jenna looked over at Adrian, who looked slightly baffled by the machine's blunt mannerisms.

The science team finally finished installing the piece.

"Rebooting," GlaDos' robotic voice said.

The machine slumped down, in a hauntingly human fashion. Suddenly it whirled back to life again.

"Good Afternoon. I am the Genetic Life-form and Disc Operating System. The time is 2:36 p.m. The indoor air quality is very poor; and the cake is currently being baked, and will be ready for the final icing phase in 57 minutes."

"GlaDos, can you please run an air exchange to clean out the Chemical-Y in the air." One of the scientists said.

"Affirmative. Commencing air quality purification and atmospheric exchange in five….four…three…two…one."

Suddenly, large vents came out of the walls and began blowing out green gas. The gas engulfed the room (and Jenna assumed the entire facility) before quickly sucking it back in. After about 10 minutes, the air was clear again.

"Air exchange and purification Complete. Current atmospheric make-up is oxygen, with 6 micrograms per cubic foot of Chemical-Y."

"Why isn't it all gone?" Knight barked at the scientists.

"Because it takes some time to fully get rid of the invisible particles. They will break down in about 36 hours."

"Whatever," Knight said, "We're leaving. Shut this damned thing down."

The scientist began typing in the computer again.

"What are you doing?" GlaDos asked, "Shutting down will result in burned cake."

"Shut down any systems beyond basic functional systems." One of the scientists said.

"I don't hate you," GlaDos said, before slumping down once again.

"Let's get the hell out of here. This place give me the creeps!" Tower said.

"You said it!" Jackson concurred.

They made their way out of the large room. They stepped over many dead scientists, all with haunting looks on their faces. They came to the main exit, where the Bravo squad was waiting to leave as well.

The Delta squad and cleanup squad was running in along with all the living employees in haz-mat suits to help get the still alive scientists secured in various rooms to the medical part of the facility. Jenna was glad she didn't have to deal with the violent and dying science team.

"All units be advised that you will be ran through a complete quarantine upon exiting. Please come through the airlock tunnel two at a time." Radio command ordered.

The marines and heading out lined up, desperate for fresh, real air. Jenna and Adrian got pushed to relatively the back, where a dead scientist was laying on the ground next to a clip-board.

Adrian looked down at the body, "What do you think they're gonna do with the bodies?"

"Probably detoxify them and clean up. It'll all probably be kept quiet," Jenna guessed, "Whatever, not our problem."

Her attention turned to the clipboard on the ground. She picked it up and began peering at the notes.

"You think you should be looking at those?" Adrian asked as Jenna began flipping through the notes.

"What's HE gonna do about it?" Jenna said, motioning to the dead guy on the floor.

"Good point," Adrian said flatly.

Jenna was amazed at what she was seeing. Apparently, the facility was big with DoD contracts. Aperture Science was developing chemical Y for biological weapons, but they were also competing with another research company on teleportation technology. The competitor was using an unknown form of energy to create a teleport system that sling-shot people from one place to another somehow. Aperture science, however, was working on Portal technology as a means of transport. They were creating direct tunnels that didn't require as much energy.

It seemed they had mastered individual portal technology, and were working on larger scale tunnels through space and time.

Jenna looked up, and was struck by a sudden realization.

Jenna shot up from her sleep. She realized it was morning and let out an exasperated cry. She ran out of her room, forgetting to even put on her shoes. She sprinted as fast as her bare feet would carry her into the radio room where Kleiner and Barney were sitting.

"YOU HAVE TO CONTACT ALYX AND GORDON!" Jenna yelled.

"Why, my dear?" Kleiner asked, looking concerned at Jenna's worried face.

"It's about the Borealis! I pulled a mission at Aperture once as a marine. They are making DIRECT tunnels to other worlds! Portals for interdimensional transport. "

Kleiner began to look like he knew what she was talking about, but Barney was confused.

"What are you saying, Jen?" Barney asked.

"The borealis didn't use a relay to port out, it TUNNELED out. They have portal technology and obviously to a large scale if they can remove a whole SHIP from dry dock! The combine are going to get to it in order to tunnel in REINFORCEMENTS from their home planet!"

"Oh lord!" Barney yelled. Kleiner was already at the radio, frantically yelling into it.

"Alyx! Gordon! This is Dr. Kleiner! Abort the mission to the borealis! The combine are going to use it go port in reinforcements. You'll be outnumbered!"

"Dr. Kleiner?" Alyx's voice came in, very fuzzy. "I can't hear you. Dr…Kl….wha….bore…..hello?!?"

Barney grabbed the radio from Kleiner.

"AL! Don't go to the borealis! You have NO CHANCE! COME BACK TO WHITE FOREST!"

"White for….Bar….What are you saying? I can't hear….dumb radio….I'm losing….HELLO?!?"

The radio suddenly went dead.

"SHIT!" Barney yelled slamming his hand on the table.

Jenna, Kleiner and Barney all stood silently in the room. They all independently prayed that Gordon and Alyx reached the Borealis before the combine, otherwise they would be outnumbered and likely doomed.

**Stay tuned for more from this storyline. I'm taking the same story from my previous fanfic, "Barney, the HECU & The Black Mesa Incident" and will put it in a half-life 2 universe! Feel free to review and subscribe to my stories! Post note: I don't own half-life and/or its characters (obviously). Credit to Valve Software for such an AWESOME series. Please make episode 3 soon and don't leave out Barney again! :-) **


End file.
